FlyTE: Transposable element discovery, annotation and population frequency in flies

Wesley fleming art sculpture

From individuals to population
Stanford University


  Ramia et al., 2012 recently designed a Gbrowse specially for the automatic analysis and representation of genetic variation across and between the D. melanogaster population: PopDrowser. PopDrowser allows to visualize genomics and population genomics data along the reference genomic sequence based on Generic Genome Browser version 2.x that offers numerous nice features. The selection of the tracks is more


   T-lex2 track

The detailed view is composed of a number of distinct tracks which stretch horizontally from one end of the display to another. Each track corresponds to a different type of genomic feature, and is distinguished by a distinctive graphical shape and color. The T-lex2 track allows to display the annotation TE insertions in population data.

TE population frequency


TE insertions not present in the reference genomic sequence are represented by red triangles while the TE insertions present in the reference genomic sequence are represented by green rectangles. The TE insertions re-annotated compared to the official TE annotation are indicated by a blue rectangle.

TE population frequency



TE population frequency




   Search for a single or multiple TE insertions
Anything that you type into the - Landmark or Region - textbox that isn't recognized as the name of a landmark will be treated as a full text search across the feature database. The searching autocompletion being activated, a menu of possible TE insertion names will pop up as you type in landmark the TE family name.

TE population frequency



All the TE insertions from a same family can also be found by searching the family name. All the annotations found are automatically display along the chromosomal D. melanogaster arms. You can click on one of the landmarks in either the graphical display or the table in order to view it in the detail view.

TE population frequency



   Download T-lex2 data for a region or the entire chromosome

TE population frequency


TE population frequency


TE population frequency